schrodinger.trajectory.rmsd2d

Module rmsd2d

A module to calculte 2D RMSD for Desmond trajectories using threading/multiprocessing. To calculate 2D RMSD for Desmond Trajectory call: from schrodinger.trajectory.rmsd2d import calc_rmsd_matrix from schrodinger.trajectory.desmondsimulation import create_simulation dsim = create_simulation("foo-out.cms", "foo_trj") rmsd_matrix = calc_rmsd_matrix(dsim, 'BACKBONE', 'BACKBONE', frame_list=None, nworkers=8, nframes=50, multiprocessing = True) Copyright (C), Schrodinger, LLC. All rights reserved.

Functions

[hide private]

calc_rmsd(r1, r2, f1=None, f2=None)

load_frame(dsim, row_block_id, col_block_id, block_size, nframes, nthreads, frame_list)

calc_rmsd_matrix_block(model, rmsd_matrix, size, row_frames, col_frames, rmsd_indices, fit_indices, i, j, block_size, nworkers)

calc_rmsd_matrix(dsim, rmsd_asl_expr, fit_asl_expr=None, frame_list=None, nworkers=1, nframes=1, multiprocessing=True)
A multithreading/multiprocessing function to calculate 2D RMSD matrix

Variables

[hide private]

__package__ = 'schrodinger.trajectory'

__warningregistry__ = {('The schrodinger.structureutil module ...

Function Details

[hide private]

calc_rmsd_matrix(dsim, rmsd_asl_expr, fit_asl_expr=None, frame_list=None, nworkers=1, nframes=1, multiprocessing=True)


A multithreading/multiprocessing function to calculate 2D RMSD matrix

    @type dsim: DesmondSimulation instance
    @param dsim:
        DesmondSimulation instance that contains reference to trajectory.

    @type rmsd_asl_expr: string
    @param rmsd_asl_expr
        The atom selection from which to indetify atom indices to be
        compared.

    @type fit_asl_expr: string
    @param fit_asl_expr:
        The atom selection from which to indetify atom indices to be
        transformed.  if fit_asl_expr is set to None, it will not
        transform the coordinates.

    @type nworkers: integer
    @param nworkers:
        Number of threads/processes used to load frames and calculate rmsd
        matrix.

    @type nframes: integer
    @param nframes:
        Number of frames handled by each worker in one run.

    @type multiprocessing: boolean
    @param multiprocessing:

    @return 2D RMSD numpy array

Variables Details

[hide private]

warningregistry

Value:

{('The schrodinger.structureutil module is deprecated. The functionali
ty has been moved to schrodinger.structutils.* modules.',
  <type 'exceptions.DeprecationWarning'>,
  25): True}